


The Line

by miera



Category: Stargate Atlantis
Genre: F/M
Language: English
Status: Completed
Published: 2011-10-31
Updated: 2011-10-31
Packaged: 2017-11-05 19:32:58
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 4,975
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/410200
Author URL: https://archiveofourown.org/users/miera/pseuds/miera
Summary: <blockquote class="userstuff">
              <p>After John returned to his own time from his trip 50,000 years into the future, he went to talk to Rodney and they put a plan in motion.</p>
            </blockquote>





	The Line

**Author's Note:**

> This fic is not entirely as developed as I would like but it's the last day of the glorious month of Sparktober and I wanted to share it.

So, it could've been worse.

John tried to settle in the tiny cave not far from the Stargate, but the ache in his injured leg was distracting. He didn't dare take anything for it, though, not when he was stuck here alone for the next several hours.

He couldn't walk, and the gate's DHD wasn't functioning. Probably because it had exploded not long after they arrived and part of it was buried in John's leg right now. Ronon and Teyla had gone to look for a village or settlement that might be able to help. John stayed near the gate, mostly hidden from view in case of any unexpected arrivals. If Atlantis called to check in on them before Teyla and Ronon got back, he could tell Elizabeth what had happened and they could send a jumper through to pick them up. If not, well he could still do that after Teyla and Ronon returned.

He was counting on Elizabeth's freaky ability to guess when he was in trouble to make Atlantis call early. Assuming Rodney whining about wanting to get out of the infirmary already didn't distract her too much. After his misadventure with the Ancient device that had temporarily made him omnipotent, Carson was keeping him under observation, although John had a feeling Carson's medical diligence was going to cave to Rodney being Rodney before long.

There was a rock sticking into his back. He squirmed, trying to find a comfortable spot, then froze in alarm.

The gate came to life. Even with Elizabeth's sixth sense, it was too early to be Atlantis checking in, so John tightened his grip on his weapon. With his luck, a bunch of Wraith would come marching through while he was alone and helpless. Being at the mercy of a hungry Wraith once was more than enough for a lifetime.

The gate crackled with energy and he wondered if there was some sort of malfunction. A lone figure came hurtling through the gate and was tossed onto the ground before the connection was cut. Cautiously, John craned his neck as he heard the newcomer groaning.

"OK, Rodney, you weren't kidding about the rough ride," he heard the man mutter. What the hell?

The man stood up stretching gingerly and then walked straight toward John's hiding place. He would've been alarmed if he hadn't been in total shock.

The newcomer was _him_. He looked... older in some way John couldn't explain. Of course, he couldn't explain coming face to face with himself either.

"I know what you're thinking," the other man said before John could manage to come up with a word. "You're not hallucinating and I'm not a Wraith or Replicator trick. I'm you from about a year from now. Well," he hedged. "A year plus fifty-thousand or so." He scratched his head. "It's kind of hard to explain."

John opened his mouth but nothing came out. His gun was still in his hand, but his mind seemed to have locked up at having his future self standing here talking to him like this was no big deal.

"I knew you'd be here, and I wanted to come when you were alone. McKay was adamant about not polluting the timeline even further. I don't have much time, I have to get back before the solar flare ends."

"So you came back in time specifically to talk to me when I can't prove any of this happened because nobody else was here?" What kind of stupid plan was that?

The other John's face scrunched up. "Yeah, I know, but Teyla and Ronon might shoot first and ask questions later. Besides, this mostly concerns you. A decision you're going to have to make." The other him crouched down. "I can't tell you too much, but it's about Elizabeth." John went cold all over. The other man looked straight at him, and John winced at the obvious pain in his face. "Atlantis is the most important thing. Forget the code, protect the city."

"What?" He shifted, trying to stand, and hissed as his bad leg shot fire through him. He wanted to jump up and grab the future him by the shoulders and shake him. "What code? What are you talking about?"

The other John shook his head. "I'm sorry, I can't tell you anything else about this. If too much changes, it could all backfire."

"You're not giving me a hell of a lot of reason to believe you here," John shot back, frustrated.

The other one stood up and shrugged helplessly. "I know. But you'll understand when... it happens."

John shivered. The finality in his voice was unnerving. They looked at each other and John knew. There was only one reason he would travel back in time to change his own history. The haunted look on his future self's face could only be from one thing.

He'd lost Elizabeth. The mere idea of it had always scared him. Being confronted by his own self and the knowledge that it would really happen was terrifying.

The visitor's watch beeped. He pulled a black device from his pocket and hit a sequence on it and the gate opened again. He paused, though, before running through it. "Oh, and go fishing with Carson. Even if you really, really don't want to."

He ran into the event horizon and vanished.

John sat for a long time staring stupidly at the gate, wondering if he had hallucinated the entire thing. Or if he'd just finally gone completely insane.

What "code" did he mean? What would that have to do with Elizabeth? Was he going to prioritize some code for something over her? Or over the city? He couldn't picture himself putting anything above Elizabeth's safety, not even Atlantis.

And this was definitely about Elizabeth's safety. He felt nauseous as he considered the possibilities that would drive him and McKay to break all kinds of rules and send a message into the past specifically to help Elizabeth. He knew she was always at risk from something in the city, but he generally thought of her as safer than him since she rarely went off-world. And of course her last off-world trip had ended badly...

Oh crap. Codes. Replicators. That had to be it. They were going to come for her, or something.

His grip tightened uselessly on his gun. He wanted to get up. He wanted to call Teyla and Ronon back and _do something_. Right now. He had to stop whatever it was from happening to Elizabeth.

He couldn't do anything. They were stuck here until Atlantis called for them or they found another way to dial the gate. He couldn't even _walk_ right now.

He ran over the conversation again and again until he had every detail fixed in his mind. By the time Teyla and Ronon returned from their fruitless search, he'd decided to say nothing to either of them yet. He'd wait until they were back in the city.

After he talked to Elizabeth.

*~*~*~*~*

"What code?"

John shook his head. "I'm not sure. He, I mean I didn't say. But..."

Elizabeth's eyes flashed with understanding. "The replicators," she said quietly.

John nodded, watching her worriedly. After the nanite infection had nearly killed her, she'd been remote and withdrawn. It had been hard as hell, watching her work through it, wishing futilely he could make it better. More than once he'd sat in the lounge or the mess with her until obscenely late hours talking about nothing or playing chess because she didn't seem to want to sleep. He'd wondered if she would sleep better if she wasn't alone ( _not_ after sex, though of course he would never in a million years say no, but he really meant just to be there if she woke up) but he never quite found the courage to say it aloud. Eventually she'd started sleeping again. Well, as much as she ever had.

Then the Ancients had kicked them out of Atlantis for months and he realized there was something worse than watching Elizabeth struggle alone, which was not seeing her at all. Since they'd gotten back they both had been acting like everything was normal again, but it wasn't. He knew she'd cut everyone off, but it still hurt that she'd avoided him too. He'd gotten used to being one of the few people she turned to for anything. He wanted to be that person for her. Him and no one else, if he was being honest with himself.

He'd missed her. More than he'd missed the city. He just didn't know how to tell her that. Or even if he should.

Elizabeth folded her arms over herself. She did that when she was thinking, or trying not to show she was scared. She walked to the window and looked out at the city. John had a feeling she spent a lot of time standing there when she was here in her quarters alone.

"Look, we know something is going to come up, something involving a code," he said, trying to come up with a plan. They both felt better when there was a plan in place of some kind. "We'll just have to be careful." He wasn't letting her off Atlantis, that was for damn sure, but he knew better than to articulate that aloud. He was going to have a hard enough time letting her out of his sight now.

Elizabeth nodded. "I'm not sure if we should tell anyone else about this."

He frowned. "We should at least talk to McKay, find out if this was even possible."

"And explain all of this how?"

"It's not like weirder stuff hasn't happened, Elizabeth."

That got a ghost of a smile. "Okay, but just Rodney for now. I don't want word of this getting out, not until we know more."

They were unlikely to know more than they did and they both knew it. He stood up from the desk chair and nodded, intending to leave. Elizabeth turned back to the window and he paused.

"I'm not going to let anything happen to you." The words came out without thought. She looked so alone, and he knew her well enough to see past the mask and know she was afraid.

Elizabeth glanced over her shoulder, her eyes haunted, reminding him that he'd already failed to protect her from the damn Replicators once. He took two steps and crossed the room to her on instinct, putting his hand on her arm. Her skin was cool under his palm. "I won't let them take you, Elizabeth."

They stood still for a moment and John actually held his breath. If she leaned toward him at all, he was going to put his arms around her. He wouldn't be able to stop himself, and he wasn't sure what would happen next. His heart thudded in his chest painfully and he realized he was almost praying she would, that she would turn to him and let him comfort her. But he couldn't make himself move and cross that line before she did.

Elizabeth moved her arm so that his hand slid down and their fingers intertwined. She squeezed his hand tightly, reminding him of that moment after the storm, grabbing onto her and not wanting to let go.

"Thanks," she said lowly, glancing briefly at him before letting his hand go.

He bit back the surge of disappointment. It mingled with relief that he hadn't done anything stupid and put them into an awkward situation. He nodded again and quietly left her quarters, his hand still tingling a little from how she'd been holding on to him.

*~*~*~*~*

By the time Ellis had come to Atlantis, it was too late to explain that a few weeks ago John had gotten a cryptic message from the future about the Replicators - maybe, anyway - delivered by his own future self while he was alone and injured. Not without sounding like he was either crazy or that he and Elizabeth and Rodney were trying to manufacture a reason to stop the mission. The attack on the Replicator planet had gone forward over Elizabeth's objections. In the aftermath, John braced himself, running through possibilities that might involve the Replicators trying to hack into the computers using a code, or doing something to their own base code, or attempting to take control of Elizabeth again, but nothing happened. The weapon hitting the city had nothing to do with codes of any kind, and the weapon ate up all their time and attention until the city rose from the planet and escaped.

Then he was standing outside the infirmary, listening as a shell-shocked Carson reported Dr. Keller had operated on Elizabeth and she was stable, but there had been extensive brain damage. "I doubt she'll ever be the same." John couldn't think straight through the grief, but he had to. Without Elizabeth he was in charge, and she wouldn't approve of him letting personal feelings get in the way of taking care of the city. He knew he couldn't let her down now.

And he knew that she would rather die than have the nanites take control of her again.

So he told Rodney and Carson not to go through with their idea to reactivate the nanites, even though it was the only thing that could bring Elizabeth back. He wondered if this was the choice he'd been warned about, to put the city ahead of Elizabeth. Dimly, as he lurched from one room to another, having not slept in a few days, he wondered if his future self had ended up having to kill Elizabeth, because reactivating the nanites had turned her into a monster.

Then of course he found out Rodney had done it anyway and Elizabeth was looking at him in horror as the reality of what they'd done sank in. But Atlantis was dying and stranded in space. They had one option and as Rodney was putting forward what had to be the most insane plan they'd ever come up with - which was saying something - John could see Elizabeth thinking the same thing he was. "Protect the city."

So they went to the Replicator home world, and miraculously managed to retrieve a ZPM. John was feeling a tiny bit less terrified at that point, until Rodney mentioned the kill code. He had it with him. They could upload it to the Replicators, reprogram them to go after the Wraith as they were originally designed to do.

It hit him like a punch. _This was it._ "Forget the code. Protect the city." It wasn't Elizabeth, it was the kill code. If they tried to upload it, something would go wrong. Something that would mean losing Elizabeth.

Elizabeth was staring at him and he knew she knew. He shook his head at Rodney. "McKay, you said you don't even know if you can hotwire the ZPM to the jumper. We need to be sure we can get back to Atlantis first."

Rodney protested but then he caught the look between John and Elizabeth. His eyes widened and he abruptly shut up and went to work in the back. As Rodney fussed and muttered and took much, much longer than hoped to rig the ZPM to the jumper, the knot that had been in John's gut for months started to dissolve. He was sure he was right.

Unfortunately Rodney didn't get the job done before Elizabeth began to sense the Replicators trying to contact her. Ronon had to stun her and it took some fancy flying before they were able to jump back to the city, get the ZPM installed and John managed just barely to land Atlantis without busting it into a million pieces.

It was hours, possibly actual days later before he finally saw Elizabeth again. There had been enormous damage to the city in their escape and contacting Earth and calling for help ate up a lot of John's time, because Elizabeth was under Marine guard still and unable to do anything even though physically she was fine.

The repairs on the city were taking up all of Rodney's time, so he hadn't had the chance to look into whether the nanites could be turned off yet. John wasn't going to let that task slide too far down the list of priorities.

She jumped up as soon as he came in, like she was bored, and he grinned a bit in spite of himself.

He glanced over his shoulder and the lieutenant outside nodded and closed the door. Elizabeth instantly asked, "What's our status?"

He ran through the most critical issues, informed her that they'd contacted Earth and help was on the way. He yawned in the middle of explaining the conversation he'd had with Caldwell and Elizabeth shook herself. "I'm sorry, you must be exhausted. Please."

She gestured to the chair and he plopped down ungracefully. Elizabeth sat on the bed opposite him and it struck him that this was exactly how they'd faced each other when he told her about his visitor.

"John?"

He met her eyes. "Do you think that was it?"

She understood immediately. "I think so." She let out a shaky laugh. "I _hope_ so."

"Me too."

She clasped her hands together. "I can't imagine another situation that would fit the warning so perfectly. A choice between a code or Atlantis? That had to be it."

He nodded. He was almost sure of it himself. Some part of him would be watching for signs, still, to ensure Elizabeth's safety. But then, that was always true.

She was staring at the floor. "John? What do you think happened?"

In the couple of hours of sleep he'd managed to get, his brain had already started churning through the possibilities. He forsaw all manner of nightmares about this in the future. Aloud, he said determinedly, "It doesn't matter." Elizabeth looked up. "We got back, the city is safe." The "for now" remained silent. The Replicators were still out there and still intent on finding and destroying Atlantis. But who knew? They might be able to find another way to upload the kill code, or find a different weapon to use against the Asurans.

And Elizabeth was here. Alive.

"You're safe," he added.

She looked away. "We don't know that for sure," she began but he held up a hand.

"McKay is monitoring the nanites closely. They're not able to hurt you, or us. He'll figure something out. And before you say something about Rodney not being omnipotent, be warned I will tell him that just to get him to work even harder to prove you wrong."

She snorted out a laugh, and then looked horribly embarrassed over it. She stood up. "You should get some rest."

He stood up too. "Night, Elizabeth." She didn't answer him right away and he paused.

"John?" Her expression had become deadly serious again. "Carson told me you argued with him and Rodney over the nanites, that you said I wouldn't have wanted them to go forward. You were right." She took a deep breath. "I can't say I'm sorry to be alive. I'm not. I'm... worried." _Scared_ , he translated mentally. "About what might happen. I need to know that you'll abide by my wishes if it comes to it again."

"It won't," he said firmly. She opened her mouth to argue and he shook his head. "It won't, Elizabeth. We're going to fix this, and you're going to be all right."

She stared up at him wordlessly. He could see the fear, he could see everything, actually, because at that moment all her walls were down. His heart pounded and he couldn't stand it. He reached for her.

Elizabeth jumped away from him. Pain lanced through him at the rejection until he saw the panic on her face. She shook her head. "You can't touch me. I might infect you."

Damn it. He balled his hands into fists for a minute. "I'm sorry. I didn't mean to..." he let the sentence die. He had no idea what he intended to say. He wasn't sorry for reaching out to her, just that something was in their way. Again.

Elizabeth folded her arms over herself. He did his best to soften his voice. "We'll fix it, Elizabeth. We will."

She looked at him and nodded. He nodded back and left, to lie in his bed and stare at the ceiling for a good while before he finally drifted to sleep.

 

*~*~*~*~*

 

Colonel Carter argued successfully with the IOA and the SGC to keep Elizabeth in Atlantis. Despite the threat she posed to the city, she was a greater threat to Earth. The last thing anyone wanted was to lead the Pegasus Replicators there. Also the best experts on the nanite technology were Sam and Rodney, so it made sense for Elizabeth to stay.

John was grateful in general that Colonel Carter was easier to get along with than most of his previous commanders in the Air Force. Sam's defense of Elizabeth made him actually like the woman.

But it was a tricky process, finding a way to shut the nanites down without Elizabeth dying. It took time, especially since as usual, emergencies kept interfering. Rodney and Sam were working as hard as they could on the problem. Meanwhile John had taken on the hobby of "keeping Elizabeth from going bonkers with boredom" to fill his off hours. They played endless rounds of cards sitting in her quarters. He knew Ronon spent time with her as well. Apparently Elizabeth had been teaching him to play chess. Teyla stopped by for tea as usual, and many of the other expedition members spent time entertaining Elizabeth with whatever they could come up with. But she remained in isolation from all of them to an extent.

She was filling most of her time studying the Ancient database, doing translations. She joked that the nanites might prove a blessing in disguise. She was one of their best experts on the Ancient language, but she hadn't had much free time to do any translating before. Now she was on a quest to find the information in the database about the ZPMs. They had to come from somewhere but McKay and Zelenka hadn't been able to uncover that information. Rodney thought it might have been erased, but Elizabeth was dogged. There had to be something.

John hadn't known how often he touched her until he absolutely couldn't. For three years the personal space between them had been shrinking. He remembered the raised eyebrow the first time he sat on her desk, but by then they'd been bumping into each other, literally, for months. He'd stolen every opportunity he could to brush up against her, craving even the slightest contact, although he hadn't admitted that to himself before. Now Elizabeth was almost holding herself rigid any time she was in close proximity to anyone, and insisting Carson, Rodney and Sam all observe protocol to keep from touching her skin.

John remembered reading somewhere that going without human touch could mess with your sanity. In this case, the worry that they were never going to find a cure for the alien technology swimming in her body was probably a bigger worry for Elizabeth.

Months went by, and the tests on Elizabeth's tissues and blood picked up their pace. Then Rodney was not sleeping for days and pushing Sam to cancel a mission and the two of them were huddled with Zelenka and Carson and even John couldn't really keep track of what they were saying. Nobody was answering his questions without using words shorter than seven syllables. He gave up and went for a run and tried to go about his day and not strain a muscle jumping every time his radio went off.

Finally, that evening, Carson pronounced them ready to start the procedure to remove the nanites permanently.

Elizabeth was lying on the bed in the infirmary. She looked scared but determined, even when Carson warned her gravely that this was likely to hurt very badly. They couldn't give her any drugs, because the nanites would process them out too fast. "I'm ready."

But she glanced at John. He nodded to her. He would keep his word, he'd honor her wishes, but this was going to work. He tried to tell her that silently and hoped he wasn't imagining the calm that spread over her face.

He and Ronon were sent outside. Teyla was off-world, searching for the Athosians and the father of her unborn baby with Lorne's team as back-up. John reflected it was probably for the best things were quiet in here for now. Elizabeth didn't need an audience for this.

The procedure was long, one of the longest things John had ever lived through. When Elizabeth began to cry out every muscle in his body tensed. When she started screaming Ronon had to grab him and hold him back from bolting inside. Then her voice died abruptly and both of them stood there frozen.

It seemed to take days before Carson and Rodney finally emerged, looking haggard but triumphant. "She fainted," Carson said before John could ask. "Just as well. We were able to complete the procedure while she was out."

His voice croaked. "Is she okay?"

Carson hesitated, making John's blood pressure spike again. "She's sleeping. I need to run some tests in a bit. We're certain the nanites were all removed, but there's no guarantee there was no damage left behind."

Ronon got to the point. "How long?"

"Two hours, at least."

Carson and Ronon urged - well, compelled, really - John to leave the infirmary and eat something. He was back an hour and a half later, sitting by Elizabeth's bedside. Rodney, Radek, Ronon and Sam were all lurking in the waiting area.

Eventually Carson came in and drew some blood, making Elizabeth wake up. John shoved his hands into his pockets to keep from taking hers. "Did it work?" she asked anxiously.

"We're about to find out," Carson told her with a reassuring smile.

The blood was sent for analysis, but Carson moved Elizabeth to the scanner and everyone but Elizabeth stared at the readout.

It was clear.

Elizabeth sat up as everyone let out a huge sigh of relief. A smile broke out across her face, but it was shaky. John could practically hear her telling herself to hold it together for a little longer. She thanked them all for what they'd done, said all the right things while everyone smiled and congratulated themselves.

They all patted her on the knee or the arm before leaving, making a point to touch her even if only briefly. John remained behind, sitting on the gurney next to Elizabeth as they waited for the final word. Carson came back and reported the blood tests were also clear. He grinned at Elizabeth. "You're free to go, love."

Elizabeth closed her eyes and a second later covered her face with her hands. Carson shot John a look and discreetly left them alone. A minute later she came out, blinking hard. John couldn't remember ever seeing her cry before. "I'm sorry. It's just a bit-"

"Overwhelming. I get it." He refrained from patting her back. Instead he slid to his feet. "You ready to get out of here?"

" _Yes_."

At the door to the infirmary John nodded to the two Marines. "Dismissed." They both grinned at Elizabeth and waved before heading off. John walked beside her but they didn't head for her quarters. She'd spent enough time there.

There was a balcony not far from her room, more private than the one outside the control room. Elizabeth stepped up to the railing and drew in a long, deep breath. John stood beside her, his arms braced on the metal. "What happens now?"

"I don't know," she confessed softly. "I think the SGC is pretty pleased with having one of their own in charge. The IOA might be torn. On the one hand, they got rid of me, but on the other they lost some control over the city." She shook her head. "I'm not terribly worried about it at the moment, to be honest." She turned and looked at him. "John, I don't know how to thank you."

He stood up straight. "You should know you don't have to."

She smiled ruefully. "I still had to say it."

They stood there, looking at each other for several moments in silence. And John just couldn't take it any more.

And he was an idiot. Because as soon as he moved Elizabeth practically lunged toward him, her arms going around his neck and holding on for dear life. He pulled her close, squeezing her so hard it couldn't have been comfortable but he couldn't make himself ease up. He could feel her heartbeat and the warmth of her skin and he just couldn't stop, not yet, not after everything. Elizabeth buried her face against his shoulder and her body shook as weeks of fear and worry finally overtook her.

 _I should've done this months ago_ , he thought to himself. _Years_. All that time, he'd been afraid of crossing the line between them, wanting Elizabeth to make the first move. What if she'd been waiting for him to do the same thing?

"God, we're dumb," he said quietly. She laughed, though it was muffled by his shirt.

He finally managed to relax his arms, letting his hand rub her back gently. His fingers had threaded through her hair without thought. Her head was nestled under his chin, so he couldn't see her face. He started to pull away to look down at her but her arms held on tightly. "Don't let go," she pleaded in a whisper.

He pulled her in close again. "Never," he promised quietly.  



End file.
